Listing 1: Solution 1: Normalized Representation
WITH DNASeq AS
(
BEGIN CALLOUT A
  SELECT P.pid, D.n AS DNAstart, 1 AS n, D.base
  FROM dbo.DNA AS D
    JOIN dbo.Patterns AS P
    ON P.n = 1 AND D.base = P.base
END CALLOUT A

  UNION ALL

BEGIN CALLOUT B
  SELECT Cur.pid, DNAstart, Cur.n + 1, DNxt.base
  FROM DNASeq AS Cur
    JOIN dbo.Patterns AS PNxt
      ON PNxt.pid = Cur.pid
      AND PNxt.n = Cur.n + 1
    JOIN dbo.DNA AS DNxt
      ON DNxt.n = DNAstart + PNxt.n - 1
     AND DNxt.base = PNxt.base
END CALLOUT B
),
PromoLen AS
(
BEGIN CALLOUT C
  SELECT pid, MAX(n) AS ln
  FROM dbo.Patterns
  GROUP BY pid
END CALLOUT C
)
BEGIN CALLOUT D
SELECT P.pname, DNAstart
FROM DNASeq AS DS
  JOIN PromoLen AS PL
    ON PL.pid = DS.pid
    AND PL.ln = DS.n
  JOIN dbo.Promoters AS P
    ON P.pid = PL.pid
ORDER BY P.pid, DNAstart
OPTION (MAXRECURSION 0);
END CALLOUT D